[Hoeze]

tl;dr: kipoiseq2 ships a py.typed marker, so type checkers read its annotations. mypy checks the package in strict mode, so every function needs annotations.

The wheel and the sdist contain kipoiseq2/py.typed. kipoiseq2/__init__.py lists Interval, Variant, Alphabet, AMINO_ACIDS, DNA, RNA, Encoder, Tokenizer, extractors and transforms in __all__. Without __all__, strict mypy rejects from kipoiseq2 import Interval, Variant, the import in README.md, because strict mode does not re-export imported names. from kipoiseq2 import * now binds only these ten names.

pyproject.toml sets strict = true for mypy. Before, mypy skipped the bodies of functions without annotations, and ignore_missing_imports = true hid every package without types. Now an override ignores only the missing types of pyfaidx, polars-bio and Biopython. The typecheck tox env still runs mypy src/kipoiseq2.

Strict mode needed few changes. _import_polars and _check_names in kipoiseq2.extractors get annotations. mypy sees the results of polars_bio.scan_vcf and polars_bio.overlap as Any, so they get the annotation LazyFrame.

Some annotations are more precise:

• The constructors of Interval and Variant take the positions as typing.SupportsIndex, so strict mypy accepts numpy integers, as the runtime did already.
• The private _resize_bounds takes the anchor as Literal["start", "center", "end"], and VariantSeqExtractor._split takes keep as Literal["left", "right", "both"].

mypy does not check the tests. About 60 test calls pass wrong types on purpose, to test the runtime checks, e.g. a float as Interval.shift(offset) or a positional use_strand. Each of them would need a # type: ignore.